The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

Abstract

The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions that swap the Xist/Tsix transcriptional unit and place their promoters in each other’s TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically up-regulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X inactivation. Our study illustrates how the genomic architecture of cis-regulatory landscapes can affect the regulation of mammalian developmental processes.

Chromatin topology and the timing of enhancer function at thehoxdlocus

“…These contacts could even resume expression of Hoxd genes in proximal limb cells, although with a truncated spatial distribution. This observation is slightly at odds with the view of TAD borders restricting the access to neighbouring enhancers and delimiting regulatory interactions (van Bemmel et al, 2019;Franke et al, 2016;Lupiáñez et al, 2015;Nora et al, 2012;Rodríguez-Carballo et al, 2017). Here, despite the presence of a strong TAD border and the inversion of CTCF sites, which clearly led to the formation of a new TAD excluding the HoxD cluster, some enhancers-promoter interactions could still occur at a sufficient level to eventually produce detectable mRNAs in the expected proximal domain, thereby indicating that such contacts have intrinsic driving forces and do not entirely depend upon an instructive 3D context.…”

Chromosome Compartments on the Inactive X Guide TAD Formation Independently of Transcription during X-Reactivation

“…Next, we investigated the regulatory landscape of the Xic from a structural perspective. The Xic is divided into two functionally opposing domains (van Bemmel et al, 2019;Galupa et al, 2020;Nora et al, 2012;Spencer et al, 2011;Tsai et al, 2008): TAD-D, which contains the noncoding genes Tsix, Xite and Linx, which are repressors of Xist; and TAD-E, which harbors Xist itself and its activators, the non-coding Jpx and Ftx and the protein-coding Rlim/Rnf12 ( Figure 5C). First, we noticed a gradual strengthening of the TAD border between TAD-D and TAD-E during reprogramming, as indicated by a drop in the insulation score ( Figure 5C).…”

Molecular basis of CTCF binding polarity in genome folding

“…Since the proposal that cohesin could enlarge chromatin loops processively 7 , cohesin complexes have been directly observed extruding DNA loops actively in vitro 8 , 9 , and found to accumulate at CTCF-binding sites in vivo 10 – 12 . Intriguingly, cohesin-dependent chromatin loops preferentially engage pairs of CTCF sites with convergent motif orientation 13 – 15 , and inverting one CTCF motif can lead to repositioning of the corresponding DNA loop 4 , 16 – 18 . Biophysical models argue that directional barriers to loop extrusion at CTCF sites are necessary to accurately simulate chromosome folding 4 – 6 .…”